Is the Amino Acid Dipeptide a Suitable Model for Investigating Structural Preferences in the Unfolded State

In view of many observations of local order within unfolded peptides and proteins, intrinsic conformational propensities of individual amino acid residues have been warranted for an understanding of how the conformational distributions in unfolded proteins affect protein folding. Various and sundry experimental and computational techniques have produced conflicting conformational sampling distributions even when similar unfolded model systems were employed. One of the most utilized model systems have been the amino acid dipeptides because the classical definition of the unfolded state was supported by the Ramachandran plot of the alanine dipeptide, which exhibited a nearly homogeneous sampling of sterically allowed conformations. Many studies on amino acid dipeptides have indicated that conformational preferences vary between different amino acids. In order to quantify these differences, we measured the amide I’ band profiles of dipeptides in water using infrared absorption, vibrational circular dichroism, and Raman spectroscopy. A conformational distribution model was utilized in order to reproduce all experimental data, which was further constrained by 3J(NHNα) and 1J(C’Cα) coupling constants. For alanine, our results suggest that it samples much less PPII-like conformations in a dipeptide than in GAG. Our experimental results were confirmed by results from Molecular Dynamics simulations. A first analysis of data obtained for other dipeptides also suggest reduced PPII fractions. We tentatively assign this to different hydration shells of blocked and unblocked peptides.